Abstract
Native potatoes are the most diverse among cultivated potato species and thus constitute a valuable source for identifying genes for potato improvement. Nevertheless, high-density mapping, needed to reveal allelic diversity, has not been performed for native Argentinian potatoes. We present a study of the genetic variability and population structure of 96 Andigena potatoes from Northwestern Argentina performed using a subset of 5035 SNPs with no missing data and full reproducibility. These high-density markers are distributed across the genome and present a good coverage of genomic regions. A Bayesian approach revealed the presence of: (I) a major group comprised of most of the Andean accessions; (II) a smaller group containing the out-group cv. Spunta and the sequenced genotype DM; and (III) a third group containing colored flesh potatoes. This grouping was also consistent when maximum likelihood trees were constructed and further confirmed by a principal coordinate analysis. A group of 19 accessions stored as Andean varieties clustered consistently with group Tuberosum accessions. This was in agreement with previous studies and we hypothesize that they may be reintroductions of European-bred long day-adapted potatoes. The present study constitutes a valuable source for allele mining of genes of interest and thus provides a tool for association mapping studies.
Highlights
Potato (Solanum tuberosum L.) is the most important non-cereal food crop and the third most important food crop for direct human consumption [1]
The depth of reads ranged from 5× to 1600× with a mean value of 18×. They were mapped altogether with genomic regions (Figure 1) using an in-house developed tool, Agrobiotechtools (Agrobiotechnology Laboratory, IPADS, CONICET-INTA) to visualize their distribution. This tool was useful for plotting density in a 1 Mbp bin and exact positions of DArTseq markers throughout the 12 potato chromosomes along with their colocalization with genomic regions
The assessment of genetic relatedness, performed by three different analyses, revealed that the collection was composed of three main subpopulations. The fact that this grouping was supported by a Bayesian approach, a genetic distance-based method, and a principal coordinate analysis, provides strong evidence for the resulting population structure
Summary
Potato (Solanum tuberosum L.) is the most important non-cereal food crop and the third most important food crop for direct human consumption [1].
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